Cytoscape Wiki
What is Level of Detail (LOD)?
In Cytoscape 2.3, a new network rendering engine is being introduced. The goal of the rendering engine is to be able to display large networks (>10,000 nodes), yet retain interactive speed. To accomplish this goal, a technique involving level of detail (LOD) is being used. Based on the number of objects (nodes and edges) being rendered, an appropriate level of detail is chosen. For example, by default, node labels (if present) are only rendered when less than 100 nodes are visible because drawing text is a relatively expensive operation. This can create some unusual behavior. If the screen currently contains 98 nodes, node labels will be displayed. If you pan across the network, such that now 101 nodes are displayed, the node labels will disappear. As another example, if the sum of rendered edges and rendered nodes is greater than or equal to a default value of 2000, a very coarse level of detail is chosen, where edges are always straight lines, nodes are always rectangles, and no antialiasing is done. The default values used to determine these thresholds can be changed by setting properties under Edit → Preferences → Properties... .
Low LOD vs High LOD
Large Network with Low LOD |
Large Network with High LOD |
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With low LOD values, all nodes are displayed as square and anti-alias is turned off. With high LOD values, anti-alias is turned on and nodes are displayed as actual shape user specified in the Visual Style.
Parameters for Controlling LOD
NOTE: The greater these thresholds become, the slower performance will become. If you work with small networks (a few hundred nodes), this shouldn't be a problem, but for large networks it will produce noticeable slowing. The various thresholds are described below.
render.coarseDetailThreshold |
If the sum of rendered nodes and rendered edges equals to or exceeds this number, a very coarse level of detail will be chosen and all other detail parameters will be ignored. If the total number of nodes and edges is below this threshold, anti-alias will be turned on; this value defaults to 2000. |
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render.nodeBorderThreshold |
If the number of rendered nodes equals to or exceeds this number, node borders will not be rendered; this value defaults to 200. |
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render.nodeLabelThreshold |
If the number of rendered nodes equals to or exceeds this number, node labels will not be rendered; this value defaults to 100. |
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render.edgeArrowThreshold |
If the number of rendered edges equals to or exceeds this number, edge arrows will not be rendered; this value defaults to 300. |
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render.edgeLabelThreshold |
If the number of rendered edges equals to or exceeds this number, edge labels will not be rendered; this value defaults to 150. |
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When printing networks or exporting to formats such as PostScript, the highest level of detail is always chosen, regardless of what is currently being displayed on the screen.
Force to Display Detail
If you want to display every detail of the network regardless of LOD values, you can use View → Show Graphics Details. This option force to display every graphics details. If the network is large, this option slows down rendering speed.